LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-584-g3e8807bee0-modified)
  using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Langevin)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style fourier
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.toluene extra/special/per/atom 1
Reading data file ...
  orthogonal box = (-18.290765 -18.163588 -18.223046) to (18.335673 18.162094 18.328654)
  2 by 1 by 2 MPI processor grid
  reading atoms ...
  5500 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  8 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  orthogonal box = (-18.290765 -18.163588 -18.223046) to (18.335673 18.162094 18.328654)
  2 by 1 by 2 MPI processor grid
  reading bonds ...
  5500 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6000 dihedrals
  reading impropers ...
  1500 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0.5     
  special bond factors coul:  0        0        0.5     
     5 = max # of 1-2 neighbors
    10 = max # of 1-3 neighbors
    16 = max # of 1-4 neighbors
    20 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_data CPU = 0.038 seconds

comm_modify vel yes

group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES

pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT

neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C C C C N N D D D D D

fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
Finding SHAKE clusters ...
    1250 = # of size 2 clusters
       0 = # of size 3 clusters
     250 = # of size 4 clusters
       0 = # of frozen angles
  find clusters CPU = 0.000 seconds

fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nve

compute cTEMP all temp/drude

thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.38201098
  grid = 40 40 40
  stencil order = 5
  estimated absolute RMS force accuracy = 0.032593379
  estimated relative force accuracy = 9.8153994e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 34263 16000
Generated 10 of 66 mixed pair_coeff terms from geometric mixing rule
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 8 8 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/thole/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 18.34 | 18.34 | 18.34 Mbytes
   Step         TotEng         KinEng          Temp          PotEng         E_bond        E_angle        E_dihed        E_impro         E_vdwl         E_coul         E_long         Press          Volume       c_cTEMP[1]     c_cTEMP[2]  
         0   11086.38       2910.7282      202.07402      8175.6516      6565.4851      20.333365      1.0706727e-06 -3299.85        4972.8631      1306116.7     -1306199.8      40273.655      48631.318      314.89553      3.1777821    
        50   4712.9507      4669.1588      324.15107      43.791911      1798.5646      670.61318      690.16968     -3276.9493      811.64296      1305983.2     -1306633.5      17164.752      48631.318      442.24309      116.13062    
       100   2865.9176      3726.4186      258.7024      -860.50097      968.86988      749.7076       860.70149     -3270.7784      427.14761      1306104.7     -1306700.9      15017.295      48631.318      385.10627      35.845766    
       150   1982.6709      3535.9729      245.48092     -1553.302       764.87123      768.15846      658.70181     -3278.7906      108.49871      1306136.5     -1306711.2      16495.35       48631.318      378.64015      10.723928    
       200   1440.0313      3240.5929      224.9745      -1800.5616      687.72504      791.29332      643.82916     -3276.9293     -99.549942      1306172.9     -1306719.8      13234.457      48631.318      350.46319      3.7468238    
       250   1103.2909      3018.4957      209.55565     -1915.2048      677.98484      825.32741      642.78894     -3278.0801     -226.18519      1306168.5     -1306725.5      8774.8985      48631.318      327.36308      1.8722382    
       300   789.07542      2827.1712      196.27316     -2038.0958      735.96704      852.72533      589.14175     -3280.0357     -374.65989      1306169       -1306730.2      2259.109       48631.318      306.85579      1.3262809    
       350   599.10156      2732.3736      189.69195     -2133.272       677.67704      863.22878      565.41671     -3280.5231     -403.28759      1306177.4     -1306733.2      7989.2298      48631.318      296.64122      1.1534508    
       400   428.259        2591.2882      179.89725     -2163.0292      676.1938       849.24498      612.34061     -3277.4703     -457.85799      1306173.6     -1306739.1      7282.067       48631.318      281.34715      1.0502884    
       450   307.26801      2534.2463      175.93719     -2226.9783      712.18268      853.98866      578.0133      -3279.7731     -533.87413      1306179.7     -1306737.2      1897.9546      48631.318      275.11312      1.0980962    
       500   234.61035      2495.1083      173.22007     -2260.4979      707.44125      878.25741      547.08395     -3281.2756     -549.04966      1306176.5     -1306739.5      2683.0674      48631.318      270.85452      1.0984802    
       550   203.35166      2445.6533      169.78671     -2242.3016      669.04278      892.85033      599.20661     -3279.0757     -559.81136      1306175.9     -1306740.4      4513.0048      48631.318      265.49462      1.0628957    
       600   205.63948      2526.5889      175.40557     -2320.9494      685.64869      887.97709      557.42292     -3280.0333     -597.34966      1306167.8     -1306742.5      2999.5902      48631.318      274.29932      1.06467      
       650   176.22872      2526.3123      175.38637     -2350.0836      714.15811      895.42113      540.39182     -3280.8567     -636.27756      1306165.7     -1306748.6      871.6774       48631.318      274.28069      1.0442136    
       700   106.97389      2441.1055      169.47099     -2334.1316      697.16694      905.51417      564.71855     -3279.6208     -631.6228       1306159.3     -1306749.6      1953.8335      48631.318      264.98931      1.0770985    
       750   76.690951      2435.6636      169.09319     -2358.9726      672.01732      934.63343      545.64013     -3281.1075     -629.89701      1306152.4     -1306752.6      3043.9839      48631.318      264.39002      1.0932608    
       800   57.611176      2456.9279      170.56944     -2399.3167      720.7706       898.68013      534.10051     -3281.5897     -659.64355      1306145.4     -1306757.1      1691.915       48631.318      266.72087      1.062284     
       850  -44.929645      2390.0608      165.92726     -2434.9904      708.70823      888.26872      537.13089     -3281.355      -665.17269      1306137.8     -1306760.3      123.07021      48631.318      259.4515       1.0516477    
       900  -96.878177      2358.8617      163.76131     -2455.7399      672.99713      868.41576      546.69479     -3280.6939     -636.79843      1306134.5     -1306760.9      1955.6777      48631.318      256.05595      1.0533552    
       950  -80.008179      2374.4504      164.84353     -2454.4585      679.60043      880.3515       548.3536      -3280.6061     -643.44488      1306125.8     -1306764.5      1510.9787      48631.318      257.72449      1.1017475    
      1000  -21.438163      2440.6725      169.44093     -2462.1107      718.57211      868.65137      555.54639     -3279.8516     -686.71619      1306126.6     -1306765       -1148.6207      48631.318      264.92972      1.1019508    
      1050   16.472052      2382.6964      165.416       -2366.2243      712.51699      913.35837      579.81684     -3280.0559     -657.12077      1306129.3     -1306764        1004.5856      48631.318      258.64077      1.0684445    
      1100   35.844947      2483.1985      172.39325     -2447.3536      685.06487      889.42273      553.73172     -3280.0177     -663.67166      1306134.3     -1306766.2      699.18341      48631.318      269.56773      1.0838279    
      1150  -4.9817685      2431.472       168.8022      -2436.4538      720.51672      868.17566      569.0991      -3280.5829     -677.999        1306133.1     -1306768.7      435.18284      48631.318      263.96959      1.0303448    
      1200  -23.902694      2443.6035      169.64441     -2467.5062      684.97203      887.58445      549.43682     -3280.3144     -679.4617       1306137.2     -1306766.9      367.10258      48631.318      265.28645      1.0344153    
      1250  -16.90345       2389.9448      165.91921     -2406.8482      722.07597      902.9008       568.35603     -3280.6829     -683.32033      1306132.9     -1306769.1      76.747791      48631.318      259.41695      1.0908734    
      1300  -1.7836672      2410.2765      167.33072     -2412.0602      706.99282      904.31929      551.23518     -3280.7552     -651.51162      1306127.3     -1306769.6      1659.0875      48631.318      261.64089      1.0701834    
      1350  -3.5683988      2446.39        169.83786     -2449.9584      686.14743      894.85851      558.36248     -3279.9941     -664.5951       1306129       -1306773.7      783.32039      48631.318      265.5696       1.0709057    
      1400  -33.38556       2400.2626      166.63552     -2433.6482      709.58743      890.68371      571.13087     -3280.1428     -674.51255      1306123.4     -1306773.8     -751.40122      48631.318      260.54528      1.0802389    
      1450  -11.218339      2405.5397      167.00188     -2416.7581      703.72879      913.2115       552.64237     -3280.9831     -649.19755      1306120.3     -1306776.4      1817.1934      48631.318      261.14729      1.0311898    
      1500  -25.972241      2435.838       169.1053      -2461.8102      689.93691      900.70559      552.63782     -3280.1497     -671.17976      1306124       -1306777.8     -98.964645      48631.318      264.45073      1.0190908    
      1550  -76.495669      2394.8123      166.25714     -2471.308       706.97642      886.07         549.91031     -3280.8434     -659.57805      1306105.9     -1306779.7     -7.1208983      48631.318      259.95399      1.0772306    
      1600  -79.551596      2395.1106      166.27784     -2474.6622      684.12387      888.93204      562.9459      -3280.1665     -665.21759      1306114.4     -1306779.6      320.58368      48631.318      260.00632      1.0425967    
      1650  -99.706786      2360.5618      163.87933     -2460.2686      706.22071      900.92655      540.36587     -3280.2308     -655.96096      1306109.7     -1306781.3      307.35325      48631.318      256.23346      1.0666695    
      1700  -69.429691      2372.1733      164.68545     -2441.603       676.79999      913.90258      581.60669     -3279.9969     -670.32972      1306115.7     -1306779.3     -204.29136      48631.318      257.50969      1.0434074    
      1750  -80.889323      2425.3582      168.37775     -2506.2475      672.89507      911.52584      523.74693     -3280.4796     -673.89995      1306122       -1306782        965.16802      48631.318      263.26479      1.1001752    
      1800  -82.418549      2361.7964      163.96505     -2444.215       716.52362      882.97349      577.92532     -3278.9278     -671.67422      1306111.6     -1306782.6     -44.942687      48631.318      256.36941      1.0636687    
      1850  -93.71135       2373.3375      164.76627     -2467.0488      713.03118      907.03728      563.38631     -3280.2577     -693.31062      1306104.6     -1306781.5     -979.94582      48631.318      257.62558      1.0628625    
      1900  -73.616605      2449.5885      170.05991     -2523.2051      683.65739      893.94382      539.90932     -3281.4317     -680.16523      1306107.9     -1306787.1      598.07127      48631.318      265.91415      1.0767053    
      1950  -66.062151      2437.3742      169.21195     -2503.4364      672.52209      877.4306       573.56317     -3279.8851     -668.54533      1306109.2     -1306787.7      733.13331      48631.318      264.61465      1.0224318    
      2000  -91.041259      2374.4095      164.8407      -2465.4508      692.13803      909.46274      574.60129     -3279.837      -672.33682      1306102.4     -1306791.8     -665.59971      48631.318      257.76295      1.0263351    
Loop time of 13.9434 on 4 procs for 2000 steps with 5500 atoms

Performance: 6.196 ns/day, 3.873 hours/ns, 143.437 timesteps/s, 788.903 katom-step/s
92.9% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 6.834      | 7.2661     | 7.6735     |  13.1 | 52.11
Bond    | 0.51152    | 0.51624    | 0.52137    |   0.5 |  3.70
Kspace  | 4.1308     | 4.6002     | 5.0111     |  17.0 | 32.99
Neigh   | 0.21304    | 0.2934     | 0.37352    |  14.6 |  2.10
Comm    | 0.50864    | 0.62395    | 0.77185    |  12.6 |  4.47
Output  | 0.0017174  | 0.001875   | 0.0022915  |   0.6 |  0.01
Modify  | 0.60119    | 0.60569    | 0.60918    |   0.4 |  4.34
Other   |            | 0.03597    |            |       |  0.26

Nlocal:           1375 ave        1381 max        1368 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost:        7803.75 ave        7856 max        7755 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs:         334465 ave      349502 max      315867 min
Histogram: 1 0 0 1 0 0 0 0 1 1

Total # of neighbors = 1337859
Ave neighs/atom = 243.24709
Ave special neighs/atom = 15.636364
Neighbor list builds = 32
Dangerous builds = 0
Total wall time: 0:00:14
